Arduino Dock 2 - A5/A4 Pins & SPI

Am I crazy or do the A5 and A4 pins not function as Digital inputs/outputs? Unless I have done something to wreck two boards... which is possible i guess. Any one have any info on this?

I have tried these pins on my Uno dock and they function as expected as Analog inputs, and Digital Inputs/Outputs with both INPUT and INPUT_PULLUP settings.

The documents say the dock functions exactly like an Uno, which is the same except for the mcu package.

EDIT:

So looking at the schematic it looks like it has to do with the Omega I2C connection through the TXS0108E level shifter chip. I have added to rc.local:omega2-ctrl gpiomux set i2c gpio
But I am still unable to successfully pull the pin to ground through a 10k resistor... the pin stays at around 3.5V

But I am still unable to successfully pull the pin to ground through a 10k resistor... the pin stays at around 3.5V

With a resistive divider you was able to determine that the TXS0108E pin is open drain and really has a 4kΩ pull up resistor inside when it is driving high :
(10kΩ * 5V / 3.5V) - 10kΩ = ~4kΩ
10 kΩ / (4kΩ + 10kΩ) * 5V = ~3.5V

IMHO some jumpers are missing from the Arduino Dock 2 by design - this is one of them (between the OE pin of TXS0108E and GND).

@György-Farkas
So this doesn't do anything.... I'm pretty sure this script doesn't get called until you actually program the mcu... and I believe the pins get reset by the omega after the script runs.

I think the issue here is I'm holding my radio IC's Chip Select pin high (to communicate with it from the arduino) and at the same time the omega is also trying to use the bus, since these two are connected and since the omega uses the spi bus to communicate with flash memory there is really no way to turn it off, with the omega still remaining useful.

I could be wrong but from all the tests I've done this seems to be the case. It just seems odd that they would break these pins out when they are totally useless on the arduino side.

@Jon-Gordon Regarding the I2C pins and using them with the ATmega MCU, it's possible and you were on the right track.
You first need to set the Omega's I2C pins to act like GPIOs (which you did) with omega2-ctrl gpiomux set i2c gpio.
Then you'll need to set them to act as input GPIOs:

gpioctl dirin 4
gpioctl dirin 5

This is crucial since the Omega will then allow these pins to float, giving the MCU an opportunity to become the I2C bus master.

For the SPI pins, yes, GPIOs 15, 16, 17 on the Omega are used to flash the MCU and are connected to the MCU's SPI pins. You can use the same gpioctl dirin command on the Omega to free the MCU's SPI lines.
Just note that your SPI device will probably need to be disconnected if you want to flash the MCU again, and you'll have to rerun the gpioctl dirin commands after you flash the MCU.

Note that GPIOs 15, 16, 17 are just GPIOs and setting them to inputs will not affect communication with the Omega's internal flash storage. That's done with the hardware SPI on GPIOs 7, 8, 9.

However, I am still unable to use A5 as an analog input and A4 as a digital input (which is what I am trying to achieve) on the arduino side as those pins seem to still be pulled up to 5VDC either through a resistor or from the TSX0108